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Physiology and Morphology




Searching the Database

In the current release of the Allen Cell Types Database, we include electrophysiological recordings from 1058 mouse cells and 279 human cells. For a subset of these cells, we also include morphological reconstructions and neuronal models. The Cell Feature Search page allows you to select cells that satisfy certain conditions and to view summary cards for those cells in a desired sorting order. From a cell's summary card, you can then navigate to pages that contain detailed electrophysiological or morphological information for that cell.



You can set filters for cell properties or data types by checking boxes and selecting one or more items from the drop-down menus at the top of the Cell Feature Search page. (Note: while the Transgenic Targeting and Donor Profile selections apply only to mouse and human cells, respectively, the rest apply to all cells.)



The following table describes the meaning of the properties available for filtering. For more details on the properties, see the Documentation.


Property nameProperty description
SpeciesSpecies of recorded cell.
AreaBrain region of recorded cell.
LayerCortical layer of recorded cell.
HemisphereHemisphere of recorded cell.
Mouse lineTransgenic driver of reporter expression.
Reporter statusExpression of transgenic reporter.
AgeAge of human donor.
Years of seizureLength of seizure history.
DonorHuman donor id.
SexSex of human donor.
DiseaseDisease state of human donor.
Ethnicity/RaceEthnicity/race of human donor.
Reconstruction typeExtent of morphological reconstruction.
Dendrite typeStatus of dendritic spines.
Apical dendrite statusExtent of apical dendrite preservation, if applicable.
Has GLIF modelExistence of GLIF model for cell.
Has all-active biophysical modelExistence of all-active biophysical model for cell.
Has perisomatic biophysical modelExistence of perisomatic biophysical model for cell.


Parallel coordinate plot of cell features

You can use the parallel coordinate plot to select cells with numerical features that satisfy certain conditions. First you choose up to five different fetures from the drop down menus under the axes, and then you select the value ranges of interest by clicking on the axes. For example, the cells selected in the figure below have Upstroke:Downstroke ratios in the range 2.0 to 5.0 and Adaptation indeces in the range 0.0 to 0.4. Each line represents a cell and the intersection with each axis indicates the value of the feature associated with that axis. Cells that do not have feature values in the selected ranges are represented by gray lines.

The "color by" drop-down menu allows you to select a feature whose value determines the line color for the cell. For example, in the figure below the lines are colored according to the Upstroke:Downstroke ratio values, so cells with higher values are represented by purple lines while cells with lower values are represented by blue lines. 


The following table describes the meaning of the properties available in the drop-down manus.For more details on the properties, see the Documentation.


Property nameProperty description
Adaptation indexRate at which firing speeds up or slows down during a stimulus.
Average firing rate (spikes/s)Average firing rate across the entire stimulus interval.
Average ISI (ms)Average interspike interval duration.
F-I curve slope (spikes/s/pA)Slope of linear fit to the frequency response of the cell versus stimulus intensity curve.
Input resistance (MΩ)Resistance of cell membrane as measured by a linear fit to responses to hyperpolarizing current steps.
Membrane time constant (ms)Time constant of exponential fit to responses to hyperpolarizing current steps.
Ramp spike time (s)Time to first spike evoked by a slow current ramp.
Resting potential (mV)Average of the pre-stimulus membrane potential.
Rheobase (pA)Minimum current amplitude of one-second-long steps that evoked an action potential.
Average contractionAverage ratio between Euclidean distance of a branch and its path length.
Maximum euclidean distance (μm)Maximum Euclidean distance from the soma to all nodes.
Normalized cortical depthDepth of the cell soma normalized between pia (0) and white matter (1).
BifurcationsNumber of points where a process splits into two daughter processes.
Soma stemsNumber of processes attached to the soma.
Parent:DaughterAverage ratio between the diameter of a daughter branch and its parent branch.

Cell summary cards

The  cell summary cards display the results of the selections specified by the filters and the parallel coordinate plot. You can sort the cards according to any cell feature by using the drop-down menus on the top right. For example, the figure below shows cards sorted in ascending value of the Parent:Daughter cell feature.

Each card provides a short summary of cell properties as well as links to pages with detailed information on the electrophysiology data and, when available, the morphology data.


The cards display the following information. For more details on the properties, see the Documentation.


Property nameProperty description
SpeciesSpecies of recorded cell.
Cell idUnique cell identifier.
AreaBrain region of recorded cell.
LayerCortical layer of recorded cell.
Dendrite typeStatus of dendritic spines.
Cre lineTransgenic driver of reporter expression (mouse cells only).
Cell reporterExpression of transgenic reporter (mouse cells only).
DonorAge and sex of donor (human cells only).
Disease stateDisease state of donor (human cells only).
Short pulse thumbnail (red)Single action potential elicited by a short (3 ms) square current injection.
Long pulse thumbnail (blue)

Subthreshold, threshold, and suprathreshold responses to a sustained (1 s) square current injection.

Morphology thumbnail

The 2D projection of the neuron reconstruction shows dendrites in red, apical dendrite in orange and axon in blue.

The scale on the right represents the normalized cortical depth, from white matter to pia. The histogram shows the density of neuronal processes as a function of depth.

Electrophysiology linkLink to page displaying the electrophysiology experiment results and, when they are available, neuronal model simulations.
Morphology linkLike to page displaying morphological properties of the cell when they are available.

Electrophysiology details page




  6. Stimulus: The stimulus injected into the cell.
Stimulus Types

Different sets of stimulation waveforms were used in order to:

    1. Linear and non-linear subthreshold properties
    2. Action potential initiation and propagation
    3. Afterhyperpolarization/afterdepolarization
  2. Understand aspects of neural response properties in vivo
    2. Ion channel states due to different resting potentials in vivo
    2. Biophysically and morphologically realistic conductance-based compartmental models

Neuronal Models





Model Name


1. Leaky Integrate and Fire (LIF)


2. LIF + Reset Rules (LIF-R)


3. LIF + Afterspike Currents (LIF-ASC)



LIF with additional Reset Rules and Afterspike Currents.





Biophysical-All Active

Biophysically realistic, single-neuron model with active conductances everywhere.

Morphology details page








Morphology Image Stack


Scale Bar



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